[gmx-users] Ordering with trjorder

[Dmitri Dubov]

Dear gmx_users,

could you clarify me how the "trjorder" procedure works? 
Manual says "For each frame of the trajectory the selected 
molecules will be reordered according to..." and so on. 
Does it mean that the ordering within each frame is 
INDEPENDENT on the prehistory and further moving of the 
group? In other words the first (the closest) molecules 
for different frames may be the different molecules?

For me, I would like to identify some molecules closest to 
the reference AT THE BEGINNING of my simulation and then 
to trace their evolution through the whole run. For this 
purpose the number of each molecule must be no changing 
from frame to frame! Can I do this with trjorder?

And one more striking thing: even when I order each frame, 
the size of output (ordered) trr-file is about twice less 
than the size of input trr!

With many thanks,
Dmitri